A report by water quality scientist Rachel Ozanne on the state of seven estuaries, the Shag, Waikouaiti, Taieri, Catlins, Kakanui and Kaikorai, was presented to the environmental science committee this week.
The estuaries' health was measured against national guidelines for the State of Environment report.
Dr Threlfall said the results provided baseline data so the council could monitor the estuaries' health in the future. There was no data on the estuaries' health prior to this study.
While the estuaries' condition was good, they were starting to have issues with heavy metals and sediment, typical effects of drainage into the waterways and land-use practices, he said.
All had some impact from phosphorus or nitrogen, "not bad", but clearly from land use upstream, he said.
"They are getting away with some stressors, but we need to keep an eye on it."
Cr Doug Brown said it was great estuaries were in good health, but the public perception of the Kakanui estuary was that it had deteriorated "a lot" with slime, algae and weeds present.
"They will struggle to relate to this report."
Dr Threlfall said the estuaries had been measured against national guidelines that were not sensitive to individual estuarine conditions.
"They need to be adapted to be site-specific, but we needed this data as a baseline."
The Kakanui was in good health, compared with national guidelines, but some issues had obviously not shown up or not been found in that study.
Doing work to ensure the river's water quality was improved and looking at storm water drainage would help.
"We do not know where else to look up until we know the cause, it could be historical like a landfill."
Dr Threlfall said the study would be repeated in about 10 years, given they were in a good state, and the work planned to improve water quality would make detecting changes in the estuaries' condition any sooner difficult.
